You have to use the auto align feature in photoshop, it will auto resize and warp one image to match the other.
I don’t have Photoshop. Are there any freeware solutions? Is there possibly a way to do it with GIMP?
You can try out this avisynth plugin, I never tried it so I don’t know how it does. It doesn’t have the warping feature though, so if one of your images has some type of distortion it will not work.